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Usai G, Fambrini M, Pugliesi C, Simoni S. Exploring the patterns of evolution: Core thoughts and focus on the saltational model. Biosystems 2024; 238:105181. [PMID: 38479653 DOI: 10.1016/j.biosystems.2024.105181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 02/29/2024] [Accepted: 03/08/2024] [Indexed: 03/18/2024]
Abstract
The Modern Synthesis, a pillar in biological thought, united Darwin's species origin concepts with Mendel's laws of character heredity, providing a comprehensive understanding of evolution within species. Highlighting phenotypic variation and natural selection, it elucidated the environment's role as a selective force, shaping populations over time. This framework integrated additional mechanisms, including genetic drift, random mutations, and gene flow, predicting their cumulative effects on microevolution and the emergence of new species. Beyond the Modern Synthesis, the Extended Evolutionary Synthesis expands perspectives by recognizing the role of developmental plasticity, non-genetic inheritance, and epigenetics. We suggest that these aspects coexist in the plant evolutionary process; in this context, we focus on the saltational model, emphasizing how saltation events, such as dichotomous saltation, chromosomal mutations, epigenetic phenomena, and polyploidy, contribute to rapid evolutionary changes. The saltational model proposes that certain evolutionary changes, such as the rise of new species, may result suddenly from single macromutations rather than from gradual changes in DNA sequences and allele frequencies within a species over time. These events, observed in domesticated and wild higher plants, provide well-defined mechanistic bases, revealing their profound impact on plant diversity and rapid evolutionary events. Notably, next-generation sequencing exposes the likely crucial role of allopolyploidy and autopolyploidy (saltational events) in generating new plant species, each characterized by distinct chromosomal complements. In conclusion, through this review, we offer a thorough exploration of the ongoing dissertation on the saltational model, elucidating its implications for our understanding of plant evolutionary processes and paving the way for continued research in this intriguing field.
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Affiliation(s)
- Gabriele Usai
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto 80, 56124, Pisa, Italy
| | - Marco Fambrini
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto 80, 56124, Pisa, Italy
| | - Claudio Pugliesi
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto 80, 56124, Pisa, Italy.
| | - Samuel Simoni
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto 80, 56124, Pisa, Italy
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2
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Zhu Y, Liu Y, Wang W, Li H, Liu C, Dou L, Wei L, Cheng W, Bao M, Yi Q, He Y. Identification and characterization of CYC2-like genes related to floral symmetric development in Tagetes erecta (Asteraceae). Gene 2023; 889:147804. [PMID: 37716585 DOI: 10.1016/j.gene.2023.147804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 09/07/2023] [Accepted: 09/13/2023] [Indexed: 09/18/2023]
Abstract
Marigold (Tagetes erecta) is an annual herbaceous flower belonging to Asteraceae, whose capitulum is composed of bilateral symmetry ray florets on the outer periphery and radial symmetry disk florets on the inside. The flower symmetry evolution from radial symmetry to bilateral symmetry has changed the morphology, inflorescence architecture and function of florets among several lineages in Asteraceae. Several studies have identified that CYC2 genes in TCP transcription factor family are the key genes regulating the flower morphogenesis, such as corolla symmetry and stamen development. Here, seven TeCYC2 genes were cloned and phylogenetically grouped into the CYC2 branch of TCP transcription family. TeCYC2c and TeCYC2d were found to be expressed specifically in ray florets, TeCYC2b was strongly expressed in both ray and disk florets, TeCYC2g was significantly higher expressed in ray florets than in disk florets, while TeCYC2a, TeCYC2e1 and TeCYC2e2 were significantly expressed in disk florets, according to an examination of the expression profile. Among the ectopic expression lines of seven TeCYC2 genes in Arabidopsis thaliana, the flower symmetry of all transgenic lines was changed from radial symmetry to bilateral symmetry, and only the reproductive growth of TeCYC2c lines was affected. In TeCYC2c transgenic Arabidopsis, the pollen sac was difficult to crack, and the filaments were shorter than the pistils, resulting in a significant decrease in the seed setting rate. All TeCYC2 proteins were localized in the nucleus. Eight pairs of interactions between TeCYC2 proteins were validated by Y2H and BiFC assays, indicating the possibility of TeCYC2 proteins forming homodimers or heterodimers to improve functional specificity. Our findings verified the main regulatory role of TeCYC2c on the development of corollas and stamen in marigold, and analyzed the interaction network of the formation mechanism of floral symmetry in two florets, which provided more insights into the expansion of CYC2 genes in the evolution of Asteraceae inflorescence and contributed to elucidate the complex regulatory network, as well as the molecular breeding concerning flower form diversity in marigold.
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Affiliation(s)
- Yu Zhu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Yuhan Liu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Wenjing Wang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Hang Li
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Cuicui Liu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Linlin Dou
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Ludan Wei
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Wenhan Cheng
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Manzhu Bao
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Qingping Yi
- Hubei Engineering Research Center for Specialty Flowers Biological Breeding, Jingchu University of Technology, Jingmen 448000, Hubei, China.
| | - Yanhong He
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China.
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3
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Keasar T, Pourtallier O, Wajnberg E. Can sociality facilitate learning of complex tasks? Lessons from bees and flowers. Philos Trans R Soc Lond B Biol Sci 2023; 378:20210402. [PMID: 36688396 PMCID: PMC9869446 DOI: 10.1098/rstb.2021.0402] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
The emergence of animal societies is a major evolutionary transition, but its implications for learning-dependent innovations are insufficiently understood. Bees, with lifestyles ranging from solitary to eusocial, are ideal models for exploring social evolution. Here, we ask how and why bees may acquire a new 'technology', foraging on morphologically complex flowers, and whether eusociality facilitates this technological shift. We consider 'complex' flowers that produce high food rewards but are difficult to access, versus 'simple' flowers offering easily accessible yet lower rewards. Complex flowers are less profitable than simple flowers to naive bees but become more rewarding after a learning period. We model how social bees optimally choose between simple and complex flowers over time, to maximize their colony's food balance. The model predicts no effect of colony size on the bees' flower choices. More foraging on complex flowers is predicted as colony longevity, its proportion of foragers, individual longevity and learning ability increase. Of these traits, only long-lived colonies and abundant foragers characterize eusocial bees. Thus, we predict that eusociality supports, but is not mandatory for, learning to exploit complex flowers. A re-analysis of a large published dataset of bee-flower interactions supports these conclusions. We discuss parallels between the evolution of insect sociality and other major transitions that provide scaffolds for learning innovations. This article is part of the theme issue 'Human socio-cultural evolution in light of evolutionary transitions'.
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Affiliation(s)
- Tamar Keasar
- Biology and Environment, University of Haifa, Oranim, Tivon 36006, Israel
| | | | - Eric Wajnberg
- INRIA, Projet Hephaistos, 06902 Sophia Antipolis, France,Inrae, 400 Route des Chappes, BP 167 06903 Sophia Antipolis Cedex, France
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4
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Carey S, Zenchyzen B, Deneka AJ, Hall JC. Nectary development in Cleome violacea. FRONTIERS IN PLANT SCIENCE 2023; 13:1085900. [PMID: 36844906 PMCID: PMC9949531 DOI: 10.3389/fpls.2022.1085900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 12/22/2022] [Indexed: 06/18/2023]
Abstract
Nectaries are a promising frontier for plant evo-devo research, and are particularly fascinating given their diversity in form, position, and secretion methods across angiosperms. Emerging model systems permit investigations of the molecular basis for nectary development and nectar secretion across a range of taxa, which addresses fundamental questions about underlying parallelisms and convergence. Herein, we explore nectary development and nectar secretion in the emerging model taxa, Cleome violacea (Cleomaceae), which exhibits a prominent adaxial nectary. First, we characterized nectary anatomy and quantified nectar secretion to establish a foundation for quantitative and functional gene experiments. Next, we leveraged RNA-seq to establish gene expression profiles of nectaries across three key stages of development: pre-anthesis, anthesis, and post-fertilization. We then performed functional studies on five genes that were putatively involved in nectary and nectar formation: CvCRABSCLAW (CvCRC), CvAGAMOUS (CvAG), CvSHATTERPROOF (CvSHP), CvSWEET9, and a highly expressed but uncharacterized transcript. These experiments revealed a high degree of functional convergence to homologues from other core Eudicots, especially Arabidopsis. CvCRC, redundantly with CvAG and CvSHP, are required for nectary initiation. Concordantly, CvSWEET9 is essential for nectar formation and secretion, which indicates that the process is eccrine based in C. violacea. While demonstration of conservation is informative to our understanding of nectary evolution, questions remain. For example, it is unknown which genes are downstream of the developmental initiators CvCRC, CvAG, and CvSHP, or what role the TCP gene family plays in nectary initiation in this family. Further to this, we have initiated a characterization of associations between nectaries, yeast, and bacteria, but more research is required beyond establishing their presence. Cleome violacea is an excellent model for continued research into nectary development because of its conspicuous nectaries, short generation time, and close taxonomic distance to Arabidopsis.
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5
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Pabón-Mora N, Suárez-Baron H, Madrigal Y, Alzate JF, González F. Expression and Functional Studies of Leaf, Floral, and Fruit Developmental Genes in Non-model Species. Methods Mol Biol 2023; 2686:365-401. [PMID: 37540370 DOI: 10.1007/978-1-0716-3299-4_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/05/2023]
Abstract
Researchers working on evolutionary developmental plant biology are inclined to choose non-model taxa to address how specific features have been acquired during ontogeny and fixed during phylogeny. In this chapter we describe methods to extract RNA, to assemble de-novo transcriptomes, to isolate orthologous genes within gene families, and to evaluate expression and function of target genes. We have successfully optimized these protocols for non-model plant species including ferns, gymnosperms, and a large assortment of angiosperms. In the latter, we have ranged a large number of families including Aristolochiaceae, Apodanthaceae, Chloranthaceae, Orchidaceae, Papaveraceae, Rubiaceae, Solanaceae, and Tropaeolaceae.
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Affiliation(s)
| | - Harold Suárez-Baron
- Instituto de Biología, Universidad de Antioquia, Medellín, Colombia
- Departamento de Ciencias Naturales y Matemáticas, Pontificia Universidad Javeriana, Cali, Colombia
| | - Yesenia Madrigal
- Instituto de Biología, Universidad de Antioquia, Medellín, Colombia
| | - Juan F Alzate
- Centro Nacional de Secuenciación Genómica-CNSG, Sede de Investigación Universitaria-SIU, Medellín, Antioquia, Colombia
| | - Favio González
- Instituto de Ciencias Naturales, Universidad Nacional de Colombia, Sede Bogotá, Bogotá, Colombia
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6
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Characterizations of a Class-I BASIC PENTACYSTEINE Gene Reveal Conserved Roles in the Transcriptional Repression of Genes Involved in Seed Development. Curr Issues Mol Biol 2022; 44:4059-4069. [PMID: 36135190 PMCID: PMC9497819 DOI: 10.3390/cimb44090278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 08/29/2022] [Accepted: 09/02/2022] [Indexed: 11/17/2022] Open
Abstract
The developmental regulation of flower organs involves the spatio-temporal regulation of floral homeotic genes. BASIC PENTACYSTEINE genes are plant-specific transcription factors that is involved in many aspects of plant development through gene transcriptional regulation. Although studies have shown that the BPC genes are involved in the developmental regulation of flower organs, little is known about their role in the formation of double-flower due. Here we characterized a Class I BPC gene (CjBPC1) from an ornamental flower—Camellia japonica. We showed that CjBPC1 is highly expressed in the central whorls of flowers in both single and doubled varieties. Overexpression of CjBPC1 in Arabidopsis thaliana caused severe defects in siliques and seeds. We found that genes involved in ovule and seed development, including SEEDSTICK, LEAFY COTYLEDON2, ABSCISIC ACID INSENSITIVE 3 and FUSCA3, were significantly down-regulated in transgenic lines. We showed that the histone 3 lysine 27 methylation levels of these downstream genes were enhanced in the transgenic plants, indicating conserved roles of CjBPC1 in recruiting the Polycomb Repression Complex for gene suppression.
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7
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Tong J, Knox EB, Morden CW, Cellinese N, Mossolem F, Zubair AS, Howarth DG. Duplication and expression patterns of CYCLOIDEA-like genes in Campanulaceae. EvoDevo 2022; 13:5. [PMID: 35125117 PMCID: PMC8819851 DOI: 10.1186/s13227-021-00189-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 12/22/2021] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
CYCLOIDEA (CYC)-like transcription factors pattern floral symmetry in most angiosperms. In core eudicots, two duplications led to three clades of CYC-like genes: CYC1, CYC2, and CYC3, with orthologs of the CYC2 clade restricting expression dorsally in bilaterally symmetrical flowers. Limited data from CYC3 suggest that they also play a role in flower symmetry in some asterids. We examine the evolution of these genes in Campanulaceae, a group that contains broad transitions between radial and bilateral floral symmetry and 180° resupination (turning upside-down by twisting pedicle).
Results
We identify here all three paralogous CYC-like clades across Campanulaceae. Similar to other core eudicots, we show that CamCYC2 duplicated near the time of the divergence of the bilaterally symmetrical and resupinate Lobelioideae. However, in non-resupinate, bilaterally symmetrical Cyphioideae, CamCYC2 appears to have been lost and CamCYC3 duplicated, suggesting a novel genetic basis for bilateral symmetry in Cyphioideae. We additionally, utilized qRT-PCR to examine the correlation between CYC-like gene expression and shifts in flower morphology in four species of Lobelioideae. As expected, CamCYC2 gene expression was dorsoventrally restricted in bilateral symmetrical flowers. However, because Lobelioideae have resupinate flowers, both CamCYC2A and CamCYC2B are highly expressed in the finally positioned ventral petal lobes, corresponding to the adaxial side of the flower relative to meristem orientation.
Conclusions
Our sequences across Campanulaceae of all three of these paralogous groups suggests that radially symmetrical Campanuloideae duplicated CYC1, Lobelioideae duplicated CYC2 and lost CYC3 early in their divergence, and that Cyphioideae lost CYC2 and duplicated CYC3. This suggests a dynamic pattern of duplication and loss of major floral patterning genes in this group and highlights the first case of a loss of CYC2 in a bilaterally symmetrical group. We illustrate here that CYC expression is conserved along the dorsoventral axis of the flower even as it turns upside-down, suggesting that at least late CYC expression is not regulated by extrinsic factors such as gravity. We additionally show that while the pattern of dorsoventral expression of each paralog remains the same, CamCYC2A is more dominant in species with shorter relative finally positioned dorsal lobes, and CamCYC2B is more dominant in species with long dorsal lobes.
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8
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Ramage E, Soza VL, Yi J, Deal H, Chudgar V, Hall BD, Di Stilio VS. Gene Duplication and Differential Expression of Flower Symmetry Genes in Rhododendron (Ericaceae). PLANTS (BASEL, SWITZERLAND) 2021; 10:1994. [PMID: 34685803 PMCID: PMC8541606 DOI: 10.3390/plants10101994] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 09/20/2021] [Accepted: 09/20/2021] [Indexed: 01/11/2023]
Abstract
Bilaterally symmetric flowers have evolved over a hundred times in angiosperms, yet orthologs of the transcription factors CYCLOIDEA (CYC), RADIALIS (RAD), and DIVARICATA (DIV) are repeatedly implicated in floral symmetry changes. We examined these candidate genes to elucidate the genetic underpinnings of floral symmetry changes in florally diverse Rhododendron, reconstructing gene trees and comparing gene expression across floral organs in representative species with radial and bilateral flower symmetries. Radially symmetric R. taxifolium Merr. and bilaterally symmetric R. beyerinckianum Koord. had four and five CYC orthologs, respectively, from shared tandem duplications. CYC orthologs were expressed in the longer dorsal petals and stamens and highly expressed in R. beyerinckianum pistils, whereas they were either ubiquitously expressed, lost from the genome, or weakly expressed in R. taxifolium. Both species had two RAD and DIV orthologs uniformly expressed across all floral organs. Differences in gene structure and expression of Rhododendron RAD compared to other asterids suggest that these genes may not be regulated by CYC orthologs. Our evidence supports CYC orthologs as the primary regulators of differential organ growth in Rhododendron flowers, while also suggesting certain deviations from the typical asterid gene regulatory network for flower symmetry.
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Affiliation(s)
- Elizabeth Ramage
- Department of Biology, University of Washington, Seattle, WA 98195, USA; (E.R.); (H.D.); (V.C.); (B.D.H.); (V.S.D.S.)
| | - Valerie L. Soza
- Department of Biology, University of Washington, Seattle, WA 98195, USA; (E.R.); (H.D.); (V.C.); (B.D.H.); (V.S.D.S.)
| | - Jing Yi
- Key Laboratory of Ecology and Environmental Science in Guangdong Higher Education, School of Life Science, South China Normal University, Guangzhou 510631, China;
| | - Haley Deal
- Department of Biology, University of Washington, Seattle, WA 98195, USA; (E.R.); (H.D.); (V.C.); (B.D.H.); (V.S.D.S.)
| | - Vaidehi Chudgar
- Department of Biology, University of Washington, Seattle, WA 98195, USA; (E.R.); (H.D.); (V.C.); (B.D.H.); (V.S.D.S.)
| | - Benjamin D. Hall
- Department of Biology, University of Washington, Seattle, WA 98195, USA; (E.R.); (H.D.); (V.C.); (B.D.H.); (V.S.D.S.)
| | - Verónica S. Di Stilio
- Department of Biology, University of Washington, Seattle, WA 98195, USA; (E.R.); (H.D.); (V.C.); (B.D.H.); (V.S.D.S.)
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9
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Qin L, Hu Y, Wang J, Wang X, Zhao R, Shan H, Li K, Xu P, Wu H, Yan X, Liu L, Yi X, Wanke S, Bowers JE, Leebens-Mack JH, dePamphilis CW, Soltis PS, Soltis DE, Kong H, Jiao Y. Insights into angiosperm evolution, floral development and chemical biosynthesis from the Aristolochia fimbriata genome. NATURE PLANTS 2021; 7:1239-1253. [PMID: 34475528 PMCID: PMC8445822 DOI: 10.1038/s41477-021-00990-2] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Accepted: 07/22/2021] [Indexed: 05/04/2023]
Abstract
Aristolochia, a genus in the magnoliid order Piperales, has been famous for centuries for its highly specialized flowers and wide medicinal applications. Here, we present a new, high-quality genome sequence of Aristolochia fimbriata, a species that, similar to Amborella trichopoda, lacks further whole-genome duplications since the origin of extant angiosperms. As such, the A. fimbriata genome is an excellent reference for inferences of angiosperm genome evolution, enabling detection of two novel whole-genome duplications in Piperales and dating of previously reported whole-genome duplications in other magnoliids. Genomic comparisons between A. fimbriata and other angiosperms facilitated the identification of ancient genomic rearrangements suggesting the placement of magnoliids as sister to monocots, whereas phylogenetic inferences based on sequence data we compiled yielded ambiguous relationships. By identifying associated homologues and investigating their evolutionary histories and expression patterns, we revealed highly conserved floral developmental genes and their distinct downstream regulatory network that may contribute to the complex flower morphology in A. fimbriata. Finally, we elucidated the genetic basis underlying the biosynthesis of terpenoids and aristolochic acids in A. fimbriata.
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Affiliation(s)
- Liuyu Qin
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yiheng Hu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jinpeng Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- School of Life Sciences and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
| | - Xiaoliang Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ran Zhao
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, China
| | - Hongyan Shan
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, China
| | - Kunpeng Li
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Peng Xu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Hanying Wu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, China
| | - Xueqing Yan
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Lumei Liu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xin Yi
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, China
| | - Stefan Wanke
- Institute of Botany, Dresden University of Technology, Dresden, Germany
| | - John E Bowers
- Department of Plant Biology, University of Georgia, Athens, GA, USA
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, USA
| | | | - Claude W dePamphilis
- Department of Biology and Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
| | - Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
- Department of Biology, University of Florida, Gainesville, FL, USA
| | - Hongzhi Kong
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yuannian Jiao
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
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10
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Xu S, Ding Y, Sun J, Zhang Z, Wu Z, Yang T, Shen F, Xue G. A high-quality genome assembly of Jasminum sambac provides insight into floral trait formation and Oleaceae genome evolution. Mol Ecol Resour 2021; 22:724-739. [PMID: 34460989 DOI: 10.1111/1755-0998.13497] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 08/23/2021] [Accepted: 08/24/2021] [Indexed: 11/29/2022]
Abstract
As one of the most economically significant Oleaceae family members, Jasminum sambac is renowned for its distinct sweet, heady fragrance. Using Illumina reads, Nanopore long reads, and HiC-sequencing, we efficiently assembled and annotated the J. sambac genome. The high-quality genome assembly consisted of a total of 507 Mb sequence (contig N50 = 17.6 Mb) with 13 pseudomolecules. A total of 21,143 protein-coding genes and 303 Mb repeat sequences were predicted. An ancient whole-genome triplication event at the base of Oleaceae (~66 million years ago [Ma], Late Cretaceous) was identified and this may have contributed to the diversification of the Oleaceae ancestor and its divergence from the Lamiales. Stress-related (e.g., WRKY) and flowering-related (e.g., MADS-box) genes were located in the triplicated regions, suggesting that the polyploidy event might have contributed adaptive potential. Genes related to terpenoid biosynthesis, for example, FTA and TPS, were observed to be duplicated to a great extent in the J. sambac genome, perhaps explaining the strong fragrance of the flowers. Copy number changes in distinct phylogenetic clades of the MADS-box family were observed in J. sambac genome, for example, AGL6- and Mα- were lost and SOC- expanded, features that might underlie the long flowering period of J. sambac. The structural genes implicated in anthocyanin biosynthesis were depleted and this may explain the absence of vivid colours in jasmine. Collectively, assembling the J. sambac genome provides new insights into the genome evolution of the Oleaceae family and provides mechanistic insights into floral properties.
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Affiliation(s)
- Shixiao Xu
- Tobacco College, Henan Agricultural University, Zhengzhou City, Henan Province, China.,Scientific Observation and Experiment Station of Tobacco Biology & Processing, Ministry of Agriculture, Zhengzhou City, Henan Province, China.,National Tobacco Cultivation & Physiology & Biochemisty Research Centre, Zhengzhou City, Henan Province, China
| | - Yongle Ding
- Tobacco College, Henan Agricultural University, Zhengzhou City, Henan Province, China.,Scientific Observation and Experiment Station of Tobacco Biology & Processing, Ministry of Agriculture, Zhengzhou City, Henan Province, China.,National Tobacco Cultivation & Physiology & Biochemisty Research Centre, Zhengzhou City, Henan Province, China
| | - Juntao Sun
- Tobacco College, Henan Agricultural University, Zhengzhou City, Henan Province, China.,Scientific Observation and Experiment Station of Tobacco Biology & Processing, Ministry of Agriculture, Zhengzhou City, Henan Province, China.,National Tobacco Cultivation & Physiology & Biochemisty Research Centre, Zhengzhou City, Henan Province, China
| | - Zhiqiang Zhang
- Tobacco College, Henan Agricultural University, Zhengzhou City, Henan Province, China.,Scientific Observation and Experiment Station of Tobacco Biology & Processing, Ministry of Agriculture, Zhengzhou City, Henan Province, China.,National Tobacco Cultivation & Physiology & Biochemisty Research Centre, Zhengzhou City, Henan Province, China
| | - Zhaoyun Wu
- Tobacco College, Henan Agricultural University, Zhengzhou City, Henan Province, China.,Scientific Observation and Experiment Station of Tobacco Biology & Processing, Ministry of Agriculture, Zhengzhou City, Henan Province, China.,National Tobacco Cultivation & Physiology & Biochemisty Research Centre, Zhengzhou City, Henan Province, China
| | - Tiezhao Yang
- Tobacco College, Henan Agricultural University, Zhengzhou City, Henan Province, China
| | - Fei Shen
- Beijing Agro-biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Gang Xue
- Tobacco College, Henan Agricultural University, Zhengzhou City, Henan Province, China.,Scientific Observation and Experiment Station of Tobacco Biology & Processing, Ministry of Agriculture, Zhengzhou City, Henan Province, China.,National Tobacco Cultivation & Physiology & Biochemisty Research Centre, Zhengzhou City, Henan Province, China
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11
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Liu X, Bourgault R, Galli M, Strable J, Chen Z, Feng F, Dong J, Molina I, Gallavotti A. The FUSED LEAVES1-ADHERENT1 regulatory module is required for maize cuticle development and organ separation. THE NEW PHYTOLOGIST 2021; 229:388-402. [PMID: 32738820 DOI: 10.1101/2020.02.11.943787] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 07/22/2020] [Indexed: 05/27/2023]
Abstract
All aerial epidermal cells in land plants are covered by the cuticle, an extracellular hydrophobic layer that provides protection against abiotic and biotic stresses and prevents organ fusion during development. Genetic and morphological analysis of the classic maize adherent1 (ad1) mutant was combined with genome-wide binding analysis of the maize MYB transcription factor FUSED LEAVES1 (FDL1), coupled with transcriptional profiling of fdl1 mutants. We show that AD1 encodes an epidermally-expressed 3-KETOACYL-CoA SYNTHASE (KCS) belonging to a functionally uncharacterized clade of KCS enzymes involved in cuticular wax biosynthesis. Wax analysis in ad1 mutants indicates that AD1 functions in the formation of very-long-chain wax components. We demonstrate that FDL1 directly binds to CCAACC core motifs present in AD1 regulatory regions to activate its expression. Over 2000 additional target genes of FDL1, including many involved in cuticle formation, drought response and cell wall organization, were also identified. Our results identify a regulatory module of cuticle biosynthesis in maize that is conserved across monocots and eudicots, and highlight previously undescribed factors in lipid metabolism, transport and signaling that coordinate organ development and cuticle formation.
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Affiliation(s)
- Xue Liu
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ, 08854-8020, USA
| | - Richard Bourgault
- Department of Biology, Algoma University, Sault Ste. Marie, ON, P6A 2G4, Canada
| | - Mary Galli
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ, 08854-8020, USA
| | - Josh Strable
- School of Integrative Plant Science, Plant Biology Section, Cornell University, Ithaca, NY, 14853, USA
| | - Zongliang Chen
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ, 08854-8020, USA
| | - Fan Feng
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ, 08854-8020, USA
| | - Jiaqiang Dong
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ, 08854-8020, USA
| | - Isabel Molina
- Department of Biology, Algoma University, Sault Ste. Marie, ON, P6A 2G4, Canada
| | - Andrea Gallavotti
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ, 08854-8020, USA
- Department of Plant Biology, Rutgers University, New Brunswick, NJ, 08901, USA
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12
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Wessinger CA, Hileman LC. Parallelism in Flower Evolution and Development. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2020. [DOI: 10.1146/annurev-ecolsys-011720-124511] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Flower evolution is characterized by widespread repetition, with adaptations to pollinator environment evolving in parallel. Recent studies have expanded our understanding of the developmental basis of adaptive floral novelties—petal fusion, bilateral symmetry, heterostyly, and floral dimensions. In this article, we describe patterns of trait evolution and review developmental genetic mechanisms underlying floral novelties. We discuss the diversity of mechanisms for parallel adaptation, the evidence for constraints on these mechanisms, and how constraints help explain observed macroevolutionary patterns. We describe parallel evolution resulting from similarities at multiple hierarchical levels—genetic, developmental, morphological, functional—which indicate general principles in floral evolution, including the central role of hormone signaling. An emerging pattern is mutational bias that may contribute to rapid patterns of parallel evolution, especially if the derived trait can result from simple degenerative mutations. We argue that such mutational bias may be less likely to govern the evolution of novelties patterned by complex developmental pathways.
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Affiliation(s)
- Carolyn A. Wessinger
- Department of Biological Sciences, University of South Carolina, Columbia, South Carolina 29208, USA
| | - Lena C. Hileman
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas 66045, USA
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13
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Ding B, Xia R, Lin Q, Gurung V, Sagawa JM, Stanley LE, Strobel M, Diggle PK, Meyers BC, Yuan YW. Developmental Genetics of Corolla Tube Formation: Role of the tasiRNA- ARF Pathway and a Conceptual Model. THE PLANT CELL 2020; 32:3452-3468. [PMID: 32917737 PMCID: PMC7610285 DOI: 10.1105/tpc.18.00471] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 08/20/2020] [Accepted: 09/08/2020] [Indexed: 05/08/2023]
Abstract
Over 80,000 angiosperm species produce flowers with petals fused into a corolla tube. The corolla tube contributes to the tremendous diversity of flower morphology and plays a critical role in plant reproduction, yet it remains one of the least understood plant structures from a developmental genetics perspective. Through mutant analyses and transgenic experiments, we show that the tasiRNA-ARF pathway is required for corolla tube formation in the monkeyflower species Mimulus lewisii Loss-of-function mutations in the M. lewisii orthologs of ARGONAUTE7 and SUPPRESSOR OF GENE SILENCING3 cause a dramatic decrease in abundance of TAS3-derived small RNAs and a moderate upregulation of AUXIN RESPONSE FACTOR3 (ARF3) and ARF4, which lead to inhibition of lateral expansion of the bases of petal primordia and complete arrest of the upward growth of the interprimordial regions, resulting in unfused corollas. Using the DR5 auxin-responsive promoter, we discovered that auxin signaling is continuous along the petal primordium base and the interprimordial region during the critical stage of corolla tube formation in the wild type, similar to the spatial pattern of MlARF4 expression. Auxin response is much weaker and more restricted in the mutant. Furthermore, exogenous application of a polar auxin transport inhibitor to wild-type floral apices disrupted petal fusion. Together, these results suggest a new conceptual model highlighting the central role of auxin-directed synchronized growth of the petal primordium base and the interprimordial region in corolla tube formation.
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Affiliation(s)
- Baoqing Ding
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, Connecticut 06269
| | - Rui Xia
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, Guangdong 510642, China
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132
| | - Qiaoshan Lin
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, Connecticut 06269
| | - Vandana Gurung
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, Connecticut 06269
| | - Janelle M Sagawa
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, Connecticut 06269
| | - Lauren E Stanley
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, Connecticut 06269
| | - Matthew Strobel
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, Connecticut 06269
| | - Pamela K Diggle
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, Connecticut 06269
| | - Blake C Meyers
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132
- Division of Plant Sciences, University of Missouri, Columbia, Missouri 65211
| | - Yao-Wu Yuan
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, Connecticut 06269
- Institute for Systems Genomics, University of Connecticut, Storrs, Connecticut 06269
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14
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Borghi M, Fernie AR. Outstanding questions in flower metabolism. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:1275-1288. [PMID: 32410253 DOI: 10.1111/tpj.14814] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 04/29/2020] [Accepted: 05/05/2020] [Indexed: 06/11/2023]
Abstract
The great diversity of flowers, their color, odor, taste, and shape, is mostly a result of the metabolic processes that occur in this reproductive organ when the flower and its tissues develop, grow, and finally die. Some of these metabolites serve to advertise flowers to animal pollinators, other confer protection towards abiotic stresses, and a large proportion of the molecules of the central metabolic pathways have bioenergetic and signaling functions that support growth and the transition to fruits and seeds. Although recent studies have advanced our general understanding of flower metabolism, several questions still await an answer. Here, we have compiled a list of open questions on flower metabolism encompassing molecular aspects, as well as topics of relevance for agriculture and the ecosystem. These questions include the study of flower metabolism through development, the biochemistry of nectar and its relevance to promoting plant-pollinator interaction, recycling of metabolic resources after flowers whiter and die, as well as the manipulation of flower metabolism by pathogens. We hope with this review to stimulate discussion on the topic of flower metabolism and set a reference point to return to in the future when assessing progress in the field.
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Affiliation(s)
- Monica Borghi
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam, 14476, Germany
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam, 14476, Germany
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15
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Phillips HR, Landis JB, Specht CD. Revisiting floral fusion: the evolution and molecular basis of a developmental innovation. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:3390-3404. [PMID: 32152629 DOI: 10.1093/jxb/eraa125] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 03/02/2020] [Indexed: 05/18/2023]
Abstract
Throughout the evolution of the angiosperm flower, developmental innovations have enabled the modification or elaboration of novel floral organs enabling subsequent diversification and expansion into new niches, for example the formation of novel pollinator relationships. One such developmental innovation is the fusion of various floral organs to form complex structures. Multiple types of floral fusion exist; each type may be the result of different developmental processes and is likely to have evolved multiple times independently across the angiosperm tree of life. The development of fused organs is thought to be mediated by the NAM/CUC3 subfamily of NAC transcription factors, which mediate boundary formation during meristematic development. The goal of this review is to (i) introduce the development of fused floral organs as a key 'developmental innovation', facilitated by a change in the expression of NAM/CUC3 transcription factors; (ii) provide a comprehensive overview of floral fusion phenotypes amongst the angiosperms, defining well-known fusion phenotypes and applying them to a systematic context; and (iii) summarize the current molecular knowledge of this phenomenon, highlighting the evolution of the NAM/CUC3 subfamily of transcription factors implicated in the development of fused organs. The need for a network-based analysis of fusion is discussed, and a gene regulatory network responsible for directing fusion is proposed to guide future research in this area.
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Affiliation(s)
- Heather R Phillips
- School of Integrative Plant Science, Section of Plant Biology and the L.H. Bailey Hortorium, Cornell University, Ithaca NY, USA
| | - Jacob B Landis
- School of Integrative Plant Science, Section of Plant Biology and the L.H. Bailey Hortorium, Cornell University, Ithaca NY, USA
| | - Chelsea D Specht
- School of Integrative Plant Science, Section of Plant Biology and the L.H. Bailey Hortorium, Cornell University, Ithaca NY, USA
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16
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Bartlett M. Looking back to look forward: protein-protein interactions and the evolution of development. THE NEW PHYTOLOGIST 2020; 225:1127-1133. [PMID: 31494948 DOI: 10.1111/nph.16179] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 08/16/2019] [Indexed: 06/10/2023]
Abstract
The evolutionary modification of development was fundamental in generating extant plant diversity. Similarly, the modification of development is a path forward to engineering the plants of the future, provided we know enough about what to modify. Understanding how extant diversity was generated will reveal productive pathways forward for modifying development. Here, I discuss four examples of developmental pathways that have been remodeled by changes to protein-protein interactions. These are cases where changes to developmental pathways have been paralleled by recent changes, selected for or engineered by humans. Extant plant diversity represents a vast treasure trove of molecular solutions to ecological problems. Mining this treasure trove will allow for the intentional modification of plant development for solving future problems.
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Affiliation(s)
- Madelaine Bartlett
- University of Massachusetts Amherst, 611 North Pleasant Street, 221 Morrill 2, Amherst, MA, 01003, USA
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17
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Preston JC, Powers B, Kostyun JL, Driscoll H, Zhang F, Zhong J. Implications of region-specific gene expression for development of the partially fused petunia corolla. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 100:158-175. [PMID: 31183889 PMCID: PMC6763366 DOI: 10.1111/tpj.14436] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Revised: 05/25/2019] [Accepted: 05/29/2019] [Indexed: 05/24/2023]
Abstract
Angiosperm petal fusion (sympetaly) has evolved multiple times independently and is associated with increased specificity between plants and their pollinators. To uncover developmental genetic changes that might have led to the evolution of sympetaly in the asterid core eudicot genus Petunia (Solanaceae), we carried out global and fine-scale gene expression analyses in different regions of the corolla. We found that, despite several similarities with the choripetalous model species Arabidopsis thaliana in the proximal-distal transcriptome, the Petunia axillaris fused and proximal corolla tube expresses several genes that in A. thaliana are associated with the distal petal region. This difference aligns with variation in petal shape and fusion across ontogeny of the two species. Moreover, differential gene expression between the unfused lobes and fused tube of P. axillaris petals revealed three strong candidate genes for sympetaly based on functional annotation in organ boundary specification. Partial silencing of one of these, the HANABA TARANU (HAN)-like gene PhGATA19, resulted in reduced fusion of Petunia hybrida petals, with silencing of both PhGATA19 and its close paralog causing premature plant senescence. Finally, detailed expression analyses for the previously characterized organ boundary gene candidate NO APICAL MERISTEM (NAM) supports the hypothesis that it establishes boundaries between most P. axillaris floral organs, with the exception of boundaries between petals.
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Affiliation(s)
- Jill C. Preston
- Department of Plant Biology, The University of Vermont, 63 Carrigan Drive, Burlington, VT 05405, USA
| | - Beck Powers
- Department of Plant Biology, The University of Vermont, 63 Carrigan Drive, Burlington, VT 05405, USA
| | - Jamie L. Kostyun
- Department of Plant Biology, The University of Vermont, 63 Carrigan Drive, Burlington, VT 05405, USA
| | - Heather Driscoll
- Bioinformatics Core, Vermont Genetics Network, Department of Biology, Norwich University, 158 Harmon Drive, Northfield, VT 05663, USA
| | - Fan Zhang
- Department of Biology, The University of Vermont, 33 Marsh Life Science, Burlington, VT 05405, USA
| | - Jinshun Zhong
- Department of Plant Biology, The University of Vermont, 63 Carrigan Drive, Burlington, VT 05405, USA
- Current address: Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linne-Weg 10, D-50829 Cologne, Germany
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18
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Presence/absence of a CACTA transposon in the CYC2c gene of two genotypes of Helianthus × multiflorus cv. “Meteor” characterized by a radiate inflorescence with different shape of disk flower corollas. Biologia (Bratisl) 2019. [DOI: 10.2478/s11756-019-00301-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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19
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Madrigal Y, Alzate JF, González F, Pabón-Mora N. Evolution of RADIALIS and DIVARICATA gene lineages in flowering plants with an expanded sampling in non-core eudicots. AMERICAN JOURNAL OF BOTANY 2019; 106:334-351. [PMID: 30845367 DOI: 10.1002/ajb2.1243] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 12/07/2018] [Indexed: 05/18/2023]
Abstract
PREMISE OF THE STUDY Bilateral symmetry in core eudicot flowers is established by the differential expression of CYCLOIDEA (CYC), DICHOTOMA (DICH), and RADIALIS (RAD), which are restricted to the dorsal portion of the flower, and DIVARICATA (DIV), restricted to the ventral and lateral petals. Little is known regarding the evolution of these gene lineages in non-core eudicots, and there are no reports on gene expression that can be used to assess whether the network predates the diversification of core eudicots. METHODS Homologs of the RAD and DIV lineages were isolated from available genomes and transcriptomes, including those of three selected non-core eudicot species, the magnoliid Aristolochia fimbriata and the monocots Cattleya trianae and Hypoxis decumbens. Phylogenetic analyses for each gene lineage were performed. RT-PCR was used to evaluate the expression and putative contribution to floral symmetry in dissected floral organs of the selected species. KEY RESULTS RAD-like genes have undergone at least two duplication events before eudicot diversification, three before monocots and at least four in Orchidaceae. DIV-like genes also duplicated twice before eudicot diversification and underwent independent duplications specific to Orchidaceae. RAD-like and DIV-like genes have differential dorsiventral expression only in C. trianae, which contrasts with the homogeneous expression in the perianth of A. fimbriata. CONCLUSIONS Our results point to a common genetic regulatory network for floral symmetry in monocots and core eudicots, while alternative genetic mechanisms are likely driving the bilateral perianth symmetry in the early-diverging angiosperm Aristolochia.
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Affiliation(s)
- Yesenia Madrigal
- Instituto de Biología, Universidad de Antioquia, AA 1226, Cl. 67 No. 53-108, Medellín, Colombia
| | - Juan Fernando Alzate
- Centro Nacional de Secuenciación Genómica, SIU, Facultad de Medicina, Universidad de Antioquia, Cl. 70 No. 52-21, Medellín, Colombia
| | - Favio González
- Universidad Nacional de Colombia, Facultad de Ciencias, Instituto de Ciencias Naturales, AA. 7495, Bogotá, Colombia
| | - Natalia Pabón-Mora
- Instituto de Biología, Universidad de Antioquia, AA 1226, Cl. 67 No. 53-108, Medellín, Colombia
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20
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Sanger TJ, Rajakumar R. How a growing organismal perspective is adding new depth to integrative studies of morphological evolution. Biol Rev Camb Philos Soc 2019; 94:184-198. [PMID: 30009397 DOI: 10.1111/brv.12442] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 06/11/2018] [Accepted: 06/14/2018] [Indexed: 01/24/2023]
Abstract
Over the past half century, the field of Evolutionary Developmental Biology, or Evo-devo, has integrated diverse fields of biology into a more synthetic understanding of morphological diversity. This has resulted in numerous insights into how development can evolve and reciprocally influence morphological evolution, as well as generated several novel theoretical areas. Although comparative by default, there remains a great gap in our understanding of adaptive morphological diversification and how developmental mechanisms influence the shape and pattern of phenotypic variation. Herein we highlight areas of research that are in the process of filling this void, and areas, if investigated more fully, that will add new insights into the diversification of morphology. At the centre of our discussion is an explicit awareness of organismal biology. Here we discuss an organismal framework that is supported by three distinct pillars. First, there is a need for Evo-devo to adopt a high-resolution phylogenetic approach in the study of morphological variation and its developmental underpinnings. Secondly, we propose that to understand the dynamic nature of morphological evolution, investigators need to give more explicit attention to the processes that generate evolutionarily relevant variation at the population level. Finally, we emphasize the need to address more thoroughly the processes that structure variation at micro- and macroevolutionary scales including modularity, morphological integration, constraint, and plasticity. We illustrate the power of these three pillars using numerous examples from both invertebrates and vertebrates to emphasize that many of these approaches are already present within the field, but have yet to be formally integrated into many research programs. We feel that the most exciting new insights will come where the traditional experimental approaches to Evo-devo are integrated more thoroughly with the principles of this organismal framework.
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Affiliation(s)
- Thomas J Sanger
- Department of Biology, Loyola University Chicago, Chicago, IL 60660, U.S.A
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21
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Plus ça change, plus c'est la même chose: The developmental evolution of flowers. Curr Top Dev Biol 2019; 131:211-238. [DOI: 10.1016/bs.ctdb.2018.11.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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22
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Fambrini M, Bellanca M, Costa Muñoz M, Usai G, Cavallini A, Pugliesi C. Ligulate inflorescence of Helianthus × multiflorus, cv. Soleil d'Or, correlates with a mis-regulation of a CYCLOIDEA gene characterised by insertion of a transposable element. PLANT BIOLOGY (STUTTGART, GERMANY) 2018; 20:956-967. [PMID: 30022587 DOI: 10.1111/plb.12876] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 07/13/2018] [Indexed: 06/08/2023]
Abstract
Members of CYCLOIDEA (CYC)/TEOSINTE BRANCHED1 (TB1) transcription factor family are essential to control flower symmetry and inflorescence architecture. In the Helianthus annuus genome, ten CYC/TB1 genes have been identified. Studies performed on mutants recognised HaCYC2c as one of the key players controlling zygomorphism in sunflower. We identified CYC2c genes in the diploid Helianthus decapetalus (HdCYC2c) and in the interspecific hybrid Helianthus × multiflorus (H × mCYC2cA and H × mCYC2cB), a triploid (2n = 3× = 51), originated from unreduced eggs of H. decapetalus fertilised by reduced H. annuus male gametes. Phylogenetic analysis showed that HdCYC2c and H × mCYC2c were placed within a CYC2 subclade together with HaCYC2c but distinct from it. The present data showed that in H. × multiflorus the allele derived from H. annuus is deleted or highly modified. The H. × multiflorus taxon exists as radiate and ligulate inflorescence types. We analysed CYC2c expression in H. decapetalus and in the cultivar 'Soleil d'Or' of H. × multiflorus, a ligulate inflorescence type with actinomorphic corolla of disk flowers transformed into a zygomorphic ray-like corolla. In H. decapetalus, the HdCYC2c gene showed differential expression between developing flower types, being up-regulated in the corolla of ray flowers in comparison to the disk flower corolla. In H. × multiflorus, an insertion of 865 bp, which is part of a CACTA transposable element, was found in the 5'-untranslated region (5'-UTR) of H × mCYC2cB. This insertion could promote, even with epigenetic mechanisms, ectopic expression of the gene throughout the inflorescence, resulting in the observed loss of actinomorphy and originating a ligulate head.
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Affiliation(s)
- M Fambrini
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
| | - M Bellanca
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
| | - M Costa Muñoz
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
- Faculty of Biology, University of Barcelona, Barcelona, Spain
| | - G Usai
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
| | - A Cavallini
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
| | - C Pugliesi
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
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23
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Abstract
The angiosperm flower develops through a modular programme which, although ancient and conserved, provides the flexibility that has allowed an almost infinite variety of floral forms to emerge. In this review, we explore the evolution of floral diversity, focusing on our recent understanding of the mechanistic basis of evolutionary change. We discuss the various ways in which flower size and floral organ size can be modified, the means by which flower shape and symmetry can change, and the ways in which floral organ position can be varied. We conclude that many challenges remain before we fully understand the ecological and molecular processes that facilitate the diversification of flower structure.
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24
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Woźniak NJ, Sicard A. Evolvability of flower geometry: Convergence in pollinator-driven morphological evolution of flowers. Semin Cell Dev Biol 2018; 79:3-15. [DOI: 10.1016/j.semcdb.2017.09.028] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 09/18/2017] [Accepted: 09/19/2017] [Indexed: 01/01/2023]
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25
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Wu M, Kostyun JL, Hahn MW, Moyle LC. Dissecting the basis of novel trait evolution in a radiation with widespread phylogenetic discordance. Mol Ecol 2018; 27:3301-3316. [PMID: 29953708 DOI: 10.1111/mec.14780] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 01/15/2018] [Accepted: 01/19/2018] [Indexed: 01/03/2023]
Abstract
Phylogenetic analyses of trait evolution can provide insight into the evolutionary processes that initiate and drive phenotypic diversification. However, recent phylogenomic studies have revealed extensive gene tree-species tree discordance, which can lead to incorrect inferences of trait evolution if only a single species tree is used for analysis. This phenomenon-dubbed "hemiplasy"-is particularly important to consider during analyses of character evolution in rapidly radiating groups, where discordance is widespread. Here, we generate whole-transcriptome data for a phylogenetic analysis of 14 species in the plant genus Jaltomata (the sister clade to Solanum), which has experienced rapid, recent trait evolution, including in fruit and nectar colour, and flower size and shape. Consistent with other radiations, we find evidence for rampant gene tree discordance due to incomplete lineage sorting (ILS) and to introgression events among the well-supported subclades. As both ILS and introgression increase the probability of hemiplasy, we perform several analyses that take discordance into account while identifying genes that might contribute to phenotypic evolution. Despite discordance, the history of fruit colour evolution in Jaltomata can be inferred with high confidence, and we find evidence of de novo adaptive evolution at individual genes associated with fruit colour variation. In contrast, hemiplasy appears to strongly affect inferences about floral character transitions in Jaltomata, and we identify candidate loci that could arise either from multiple lineage-specific substitutions or standing ancestral polymorphisms. Our analysis provides a generalizable example of how to manage discordance when identifying loci associated with trait evolution in a radiating lineage.
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Affiliation(s)
- Meng Wu
- Department of Biology, Indiana University, Bloomington, Indiana
| | - Jamie L Kostyun
- Department of Biology, Indiana University, Bloomington, Indiana
- Department of Plant Biology, University of Vermont, Burlington, Vermont
| | - Matthew W Hahn
- Department of Biology, Indiana University, Bloomington, Indiana
- Department of Computer Science, Indiana University, Bloomington, Indiana
| | - Leonie C Moyle
- Department of Biology, Indiana University, Bloomington, Indiana
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Ronse De Craene L. Understanding the role of floral development in the evolution of angiosperm flowers: clarifications from a historical and physico-dynamic perspective. JOURNAL OF PLANT RESEARCH 2018; 131:367-393. [PMID: 29589194 DOI: 10.1007/s10265-018-1021-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 01/14/2018] [Indexed: 05/26/2023]
Abstract
Flower morphology results from the interaction of an established genetic program, the influence of external forces induced by pollination systems, and physical forces acting before, during and after initiation. Floral ontogeny, as the process of development from a meristem to a fully developed flower, can be approached either from a historical perspective, as a "recapitulation of the phylogeny" mainly explained as a process of genetic mutations through time, or from a physico-dynamic perspective, where time, spatial pressures, and growth processes are determining factors in creating the floral morphospace. The first (historical) perspective clarifies how flower morphology is the result of development over time, where evolutionary changes are only possible using building blocks that are available at a certain stage in the developmental history. Flowers are regulated by genetically determined constraints and development clarifies specific transitions between different floral morphs. These constraints are the result of inherent mutations or are induced by the interaction of flowers with pollinators. The second (physico-dynamic) perspective explains how changes in the physical environment of apical meristems create shifts in ontogeny and this is reflected in the morphospace of flowers. Changes in morphology are mainly induced by shifts in space, caused by the time of initiation (heterochrony), pressure of organs, and alterations of the size of the floral meristem, and these operate independently or in parallel with genetic factors. A number of examples demonstrate this interaction and its importance in the establishment of different floral forms. Both perspectives are complementary and should be considered in the understanding of factors regulating floral development. It is suggested that floral evolution is the result of alternating bursts of physical constraints and genetic stabilization processes following each other in succession. Future research needs to combine these different perspectives in understanding the evolution of floral systems and their diversification.
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Jiang P, Rausher M. Two genetic changes in cis-regulatory elements caused evolution of petal spot position in Clarkia. NATURE PLANTS 2018; 4:14-22. [PMID: 29298993 DOI: 10.1038/s41477-017-0085-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 11/29/2017] [Indexed: 06/07/2023]
Abstract
A major premise in evolutionary developmental biology is that regulatory changes, often involving cis-regulatory elements, are responsible for much morphological evolution. This premise is supported by recent investigations of animal development, but information is just beginning to accumulate regarding whether it also applies to the evolution of plant morphology1-4. Here, we identify the genetic differences between species in the genus Clarkia that are responsible for evolutionary change in an ecologically important element of floral colour patterns: spot position. The evolutionary shift in spot position was due to two simple genetic changes that resulted in the appearance of a transcription factor binding site mutation in the R2R3 Myb gene that changes spot formation. These genetic changes caused R2R3 Myb to be activated by a different transcription factor that is expressed in a different position in the petal. These results suggest that the regulatory rewiring paradigm is as applicable to plants as it is to animals, and support the hypothesis that cis-regulatory changes may often play a role in plant morphological evolution.
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Affiliation(s)
- Peng Jiang
- Biology Department, Duke University, Durham, NC, USA.
| | - Mark Rausher
- Biology Department, Duke University, Durham, NC, USA
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28
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Chanderbali AS, Berger BA, Howarth DG, Soltis DE, Soltis PS. Evolution of floral diversity: genomics, genes and gamma. Philos Trans R Soc Lond B Biol Sci 2017; 372:rstb.2015.0509. [PMID: 27994132 DOI: 10.1098/rstb.2015.0509] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/17/2016] [Indexed: 11/12/2022] Open
Abstract
A salient feature of flowering plant diversification is the emergence of a novel suite of floral features coinciding with the origin of the most species-rich lineage, Pentapetalae. Advances in phylogenetics, developmental genetics and genomics, including new analyses presented here, are helping to reconstruct the specific evolutionary steps involved in the evolution of this clade. The enormous floral diversity among Pentapetalae appears to be built on a highly conserved ground plan of five-parted (pentamerous) flowers with whorled phyllotaxis. By contrast, lability in the number and arrangement of component parts of the flower characterize the early-diverging eudicot lineages subtending Pentapetalae. The diversification of Pentapetalae also coincides closely with ancient hexaploidy, referred to as the gamma whole-genome triplication, for which the phylogenetic timing, mechanistic details and molecular evolutionary consequences are as yet not fully resolved. Transcription factors regulating floral development often persist in duplicate or triplicate in gamma-derived genomes, and both individual genes and whole transcriptional programmes exhibit a shift from broadly overlapping to tightly defined expression domains in Pentapetalae flowers. Investigations of these changes associated with the origin of Pentapetalae can lead to a more comprehensive understanding of what is arguably one of the most important evolutionary diversification events within terrestrial plants.This article is part of the themed issue 'Evo-devo in the genomics era, and the origins of morphological diversity'.
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Affiliation(s)
- Andre S Chanderbali
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA.,Department of Biology, University of Florida, Gainesville, FL 32611, USA
| | - Brent A Berger
- Department of Biological Sciences, St John's University, Queens, NY 11439, USA
| | - Dianella G Howarth
- Department of Biological Sciences, St John's University, Queens, NY 11439, USA
| | - Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA.,Department of Biology, University of Florida, Gainesville, FL 32611, USA.,Genetics Institute, University of Florida, Gainesville, FL 32610, USA
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA .,Genetics Institute, University of Florida, Gainesville, FL 32610, USA
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29
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Berger BA, Ricigliano VA, Savriama Y, Lim A, Thompson V, Howarth DG. Geometric morphometrics reveals shifts in flower shape symmetry and size following gene knockdown of CYCLOIDEA and ANTHOCYANIDIN SYNTHASE. BMC PLANT BIOLOGY 2017; 17:205. [PMID: 29149840 PMCID: PMC5693587 DOI: 10.1186/s12870-017-1152-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 11/07/2017] [Indexed: 05/14/2023]
Abstract
BACKGROUND While floral symmetry has traditionally been assessed qualitatively, recent advances in geometric morphometrics have opened up new avenues to specifically quantify flower shape and size using robust multivariate statistical methods. In this study, we examine, for the first time, the ability of geometric morphometrics to detect morphological differences in floral dorsoventral asymmetry following virus-induced gene silencing (VIGS). Using Fedia graciliflora Fisch. & Meyer (Valerianaceae) as a model, corolla shape of untreated flowers was compared using canonical variate analysis to knockdown phenotypes of CYCLOIDEA2A (FgCYC2A), ANTHOCYANIDIN SYNTHASE (FgANS), and empty vector controls. RESULTS Untreated flowers and all VIGS treatments were morphologically distinct from each other, suggesting that VIGS may cause subtle shifts in floral shape. Knockdowns of FgCYC2A were the most dramatic, affecting the position of dorsal petals in relation to lateral petals, thereby resulting in more actinomorphic-like flowers. Additionally, FgANS knockdowns developed larger flowers with wider corolla tube openings. CONCLUSIONS These results provide a method to quantify the role that specific genes play in the developmental pathway affecting the dorsoventral axis of symmetry in zygomorphic flowers. Additionally, they suggest that ANS may have an unintended effect on floral size and shape.
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Affiliation(s)
- Brent A. Berger
- Department of Biological Sciences, St. John’s University, 8000 Utopia Parkway, Queens, NY 11439 USA
| | | | - Yoland Savriama
- Department of Biological Sciences, St. John’s University, 8000 Utopia Parkway, Queens, NY 11439 USA
- Institute of Biotechnology, University of Helsinki, PO Box 56 (Viikinkaari 5), FI-00014 Helsinki, Finland
| | - Aedric Lim
- Department of Biological Sciences, St. John’s University, 8000 Utopia Parkway, Queens, NY 11439 USA
| | - Veronica Thompson
- Department of Biological Sciences, St. John’s University, 8000 Utopia Parkway, Queens, NY 11439 USA
| | - Dianella G. Howarth
- Department of Biological Sciences, St. John’s University, 8000 Utopia Parkway, Queens, NY 11439 USA
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Jablonski D. Approaches to Macroevolution: 2. Sorting of Variation, Some Overarching Issues, and General Conclusions. Evol Biol 2017; 44:451-475. [PMID: 29142334 PMCID: PMC5661022 DOI: 10.1007/s11692-017-9434-7] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 10/04/2017] [Indexed: 11/08/2022]
Abstract
Approaches to macroevolution require integration of its two fundamental components, within a hierarchical framework. Following a companion paper on the origin of variation, I here discuss sorting within an evolutionary hierarchy. Species sorting-sometimes termed species selection in the broad sense, meaning differential origination and extinction owing to intrinsic biological properties-can be split into strict-sense species selection, in which rate differentials are governed by emergent, species-level traits such as geographic range size, and effect macroevolution, in which rates are governed by organism-level traits such as body size; both processes can create hitchhiking effects, indirectly causing the proliferation or decline of other traits. Several methods can operationalize the concept of emergence, so that rigorous separation of these processes is increasingly feasible. A macroevolutionary tradeoff, underlain by the intrinsic traits that influence evolutionary dynamics, causes speciation and extinction rates to covary in many clades, resulting in evolutionary volatility of some clades and more subdued behavior of others; the few clades that break the tradeoff can achieve especially prolific diversification. In addition to intrinsic biological traits at multiple levels, extrinsic events can drive the waxing and waning of clades, and the interaction of traits and events are difficult but important to disentangle. Evolutionary trends can arise in many ways, and at any hierarchical level; descriptive models can be fitted to clade trajectories in phenotypic or functional spaces, but they may not be diagnostic regarding processes, and close attention must be paid to both leading and trailing edges of apparent trends. Biotic interactions can have negative or positive effects on taxonomic diversity within a clade, but cannot be readily extrapolated from the nature of such interactions at the organismic level. The relationships among macroevolutionary currencies through time (taxonomic richness, morphologic disparity, functional variety) are crucial for understanding the nature of evolutionary diversification. A novel approach to diversity-disparity analysis shows that taxonomic diversifications can lag behind, occur in concert with, or precede, increases in disparity. Some overarching issues relating to both the origin and sorting of clades and phenotypes include the macroevolutionary role of mass extinctions, the potential differences between plant and animal macroevolution, whether macroevolutionary processes have changed through geologic time, and the growing human impact on present-day macroevolution. Many challenges remain, but progress is being made on two of the key ones: (a) the integration of variation-generating mechanisms and the multilevel sorting processes that act on that variation, and (b) the integration of paleontological and neontological approaches to historical biology.
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Affiliation(s)
- David Jablonski
- Department of Geophysical Sciences, University of Chicago, 5734 South Ellis Avenue, Chicago, IL 60637 USA
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31
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Berger BA, Han J, Sessa EB, Gardner AG, Shepherd KA, Ricigliano VA, Jabaily RS, Howarth DG. The unexpected depths of genome-skimming data: A case study examining Goodeniaceae floral symmetry genes. APPLICATIONS IN PLANT SCIENCES 2017; 5:apps.1700042. [PMID: 29109919 PMCID: PMC5664964 DOI: 10.3732/apps.1700042] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 09/07/2017] [Indexed: 05/20/2023]
Abstract
PREMISE OF THE STUDY The use of genome skimming allows systematists to quickly generate large data sets, particularly of sequences in high abundance (e.g., plastomes); however, researchers may be overlooking data in low abundance that could be used for phylogenetic or evo-devo studies. Here, we present a bioinformatics approach that explores the low-abundance portion of genome-skimming next-generation sequencing libraries in the fan-flowered Goodeniaceae. METHODS Twenty-four previously constructed Goodeniaceae genome-skimming Illumina libraries were examined for their utility in mining low-copy nuclear genes involved in floral symmetry, specifically the CYCLOIDEA (CYC)-like genes. De novo assemblies were generated using multiple assemblers, and BLAST searches were performed for CYC1, CYC2, and CYC3 genes. RESULTS Overall Trinity, SOAPdenovo-Trans, and SOAPdenovo implementing lower k-mer values uncovered the most data, although no assembler consistently outperformed the others. Using SOAPdenovo-Trans across all 24 data sets, we recovered four CYC-like gene groups (CYC1, CYC2, CYC3A, and CYC3B) from a majority of the species. Alignments of the fragments included the entire coding sequence as well as upstream and downstream regions. DISCUSSION Genome-skimming data sets can provide a significant source of low-copy nuclear gene sequence data that may be used for multiple downstream applications.
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Affiliation(s)
- Brent A. Berger
- Department of Biological Sciences, St. John’s University, 8000 Utopia Parkway, Queens, New York 11439 USA
| | - Jiahong Han
- Department of Biological Sciences, St. John’s University, 8000 Utopia Parkway, Queens, New York 11439 USA
| | - Emily B. Sessa
- Department of Biology, University of Florida, Box 118525, Gainesville, Florida 32611 USA
| | - Andrew G. Gardner
- Department of Biological Sciences, California State University, Stanislaus, One University Circle, Turlock, California 95382 USA
| | - Kelly A. Shepherd
- Western Australian Herbarium, Department of Biodiversity, Conservation and Attractions, 17 Dick Perry Avenue, Kensington 6151, Western Australia, Australia
| | - Vincent A. Ricigliano
- USDA-ARS Carl Hayden Bee Research Center, 2000 E. Allen Road, Tucson, Arizona 85719 USA
| | - Rachel S. Jabaily
- Department of Biology, Rhodes College, 2000 N. Parkway, Memphis, Tennessee 38112 USA
| | - Dianella G. Howarth
- Department of Biological Sciences, St. John’s University, 8000 Utopia Parkway, Queens, New York 11439 USA
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Dhaka N, Bhardwaj V, Sharma MK, Sharma R. Evolving Tale of TCPs: New Paradigms and Old Lacunae. FRONTIERS IN PLANT SCIENCE 2017; 8:479. [PMID: 28421104 PMCID: PMC5376618 DOI: 10.3389/fpls.2017.00479] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2016] [Accepted: 03/20/2017] [Indexed: 05/03/2023]
Abstract
Teosinte Branched1/Cycloidea/Proliferating cell factors (TCP) genes are key mediators of genetic innovations underlying morphological novelties, stress adaptation, and evolution of immune response in plants. They have a remarkable ability to integrate and translate diverse endogenous, and environmental signals with high fidelity. Compilation of studies, aimed at elucidating the mechanism of TCP functions, shows that it takes an amalgamation and interplay of several different factors, regulatory processes and pathways, instead of individual components, to achieve the incredible functional diversity and specificity, demonstrated by TCP proteins. Through this minireview, we provide a brief description of key structural features and molecular components, known so far, that operate this conglomerate, and highlight the important conceptual challenges and lacunae in TCP research.
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Affiliation(s)
- Namrata Dhaka
- Crop Genetics & Informatics Group, School of Computational and Integrative SciencesJawaharlal Nehru University, New Delhi, India
| | - Vasudha Bhardwaj
- Crop Genetics & Informatics Group, School of BiotechnologyJawaharlal Nehru University, New Delhi, India
| | - Manoj K. Sharma
- Crop Genetics & Informatics Group, School of BiotechnologyJawaharlal Nehru University, New Delhi, India
| | - Rita Sharma
- Crop Genetics & Informatics Group, School of Computational and Integrative SciencesJawaharlal Nehru University, New Delhi, India
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Abstract
The origin of the flower was a key innovation in the history of complex organisms, dramatically altering Earth's biota. Advances in phylogenetics, developmental genetics, and genomics during the past 25 years have substantially advanced our understanding of the evolution of flowers, yet crucial aspects of floral evolution remain, such as the series of genetic and morphological changes that gave rise to the first flowers; the factors enabling the origin of the pentamerous eudicot flower, which characterizes ∼70% of all extant angiosperm species; and the role of gene and genome duplications in facilitating floral innovations. A key early concept was the ABC model of floral organ specification, developed by Elliott Meyerowitz and Enrico Coen and based on two model systems,Arabidopsis thalianaandAntirrhinum majus Yet it is now clear that these model systems are highly derived species, whose molecular genetic-developmental organization must be very different from that of ancestral, as well as early, angiosperms. In this article, we will discuss how new research approaches are illuminating the early events in floral evolution and the prospects for further progress. In particular, advancing the next generation of research in floral evolution will require the development of one or more functional model systems from among the basal angiosperms and basal eudicots. More broadly, we urge the development of "model clades" for genomic and evolutionary-developmental analyses, instead of the primary use of single "model organisms." We predict that new evolutionary models will soon emerge as genetic/genomic models, providing unprecedented new insights into floral evolution.
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PIñeyro-Nelson A, Almeida AMRD, Sass C, Iles WJD, Specht CD. Change of Fate and Staminodial Laminarity as Potential Agents of Floral Diversification in the Zingiberales. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2017; 328:41-54. [PMID: 28120453 DOI: 10.1002/jez.b.22724] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 11/30/2016] [Accepted: 12/02/2016] [Indexed: 12/30/2022]
Abstract
The evolution of floral morphology in the monocot order Zingiberales shows a trend in which androecial whorl organs are progressively modified into variously conspicuous "petaloid" structures with differing degrees of fertility. Petaloidy of androecial members results from extensive laminarization of an otherwise radially symmetric structure. The genetic basis of the laminarization of androecial members has been addressed through recent candidate gene studies focused on understanding the spatiotemporal expression patterns of genes known to be necessary to floral organ formation. Here, we explore the correlation between gene duplication events and floral and inflorescence morphological diversification across the Zingiberales by inferring ancestral character states and gene copy number using the most widely accepted phylogenetic hypotheses. Our results suggest that the duplication and differential loss of GLOBOSA (GLO) copies is correlated with a change in the degree of the laminarization of androecial members. We also find an association with increased diversification in most families. We hypothesize that retention of paralogs in flower development genes could have led to a developmental shift affecting androecial organs with potential adaptive consequences, thus favoring diversification in some lineages but not others.
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Affiliation(s)
- Alma PIñeyro-Nelson
- Department of Food and Animal Production, Autonomous Metropolitan University, Xochimilco, Mexico City, Mexico
- Department of Plant and Microbial Biology, Department of Integrative Biology, and the University and Jepson Herbaria, University of California-Berkeley, Berkeley, California
| | - Ana Maria Rocha De Almeida
- Programa de Pós-Graduação em Genética e Biodiversidade, Universidade Federal da Bahia, Rua Barão de Geremoabo, Salvador/BA, Brazil
- Department of Biological Sciences, California State University East Bay (CSUEB), Hayward, California
| | - Chodon Sass
- Department of Plant and Microbial Biology, Department of Integrative Biology, and the University and Jepson Herbaria, University of California-Berkeley, Berkeley, California
| | - William James Donaldson Iles
- Department of Plant and Microbial Biology, Department of Integrative Biology, and the University and Jepson Herbaria, University of California-Berkeley, Berkeley, California
| | - Chelsea Dvorak Specht
- Department of Plant and Microbial Biology, Department of Integrative Biology, and the University and Jepson Herbaria, University of California-Berkeley, Berkeley, California
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do Valle Capelli N, Alonso Rodrigues B, Demarco D. Stipules in Apocynaceae: an ontogenetic perspective. AOB PLANTS 2017; 9:plw083. [PMID: 28694936 PMCID: PMC5499672 DOI: 10.1093/aobpla/plw083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 02/06/2017] [Indexed: 06/07/2023]
Abstract
Stipules are leaf structures common in many groups of plants that can take a variety of forms. In Gentianales, interpetiolar stipules are considered a synapomorphy of Rubiaceae; however, some reports in the literature refer to their presence in other families. The goal of this study was to analyze the development of leaf primordia to investigate the possible presence of reduced or modified stipules in Apocynaceae. Shoot apices of 12 genera were analyzed under light and scanning electron microscopy comparatively with one species of Rubiaceae. Early in their development, leaf primordia form two lateral expansions at the base of the petiole (stipules) that give rise to colleters in 11 of the 12 genera of Apocynaceae studied, similarly to the Rubiaceae species. The basal genera have pairs of stipules modified into colleters positioned laterally to the petiole, while other species belonging to the derived subfamilies have interpetiolar stipules that each project towards the opposite stipule and merge, forming a sheathing stipule and from this arc the interpetiolar colleters originate. The ontogenetic study proved for the first time that Apocynaceae is a stipulate family whose stipules are modified into colleters and their absence might be a secondary loss, changing the interpretation of stipule evolution in Gentianales.
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Affiliation(s)
- Natalie do Valle Capelli
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo 05508-090, Brazil
| | - Bruna Alonso Rodrigues
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo 05508-090, Brazil
| | - Diego Demarco
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo 05508-090, Brazil
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Bello MA, Cubas P, Álvarez I, Sanjuanbenito G, Fuertes-Aguilar J. Evolution and Expression Patterns of CYC/TB1 Genes in Anacyclus: Phylogenetic Insights for Floral Symmetry Genes in Asteraceae. FRONTIERS IN PLANT SCIENCE 2017; 8:589. [PMID: 28487706 PMCID: PMC5403951 DOI: 10.3389/fpls.2017.00589] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 03/31/2017] [Indexed: 05/20/2023]
Abstract
Homologs of the CYC/TB1 gene family have been independently recruited many times across the eudicots to control aspects of floral symmetry The family Asteraceae exhibits the largest known diversification in this gene paralog family accompanied by a parallel morphological floral richness in its specialized head-like inflorescence. In Asteraceae, whether or not CYC/TB1 gene floral symmetry function is preserved along organismic and gene lineages is unknown. In this study, we used phylogenetic, structural and expression analyses focused on the highly derived genus Anacyclus (tribe Anthemidae) to address this question. Phylogenetic reconstruction recovered eight main gene lineages present in Asteraceae: two from CYC1, four from CYC2 and two from CYC3-like genes. The species phylogeny was recovered in most of the gene lineages, allowing the delimitation of orthologous sets of CYC/TB1 genes in Asteraceae. Quantitative real-time PCR analysis indicated that in Anacyclus three of the four isolated CYC2 genes are more highly expressed in ray flowers. The expression of the four AcCYC2 genes overlaps in several organs including the ligule of ray flowers, as well as in anthers and ovules throughout development.
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Affiliation(s)
- María A. Bello
- Plant Evolutionary Biology Group, Real Jardín Botánico (CSIC)Madrid, Spain
| | - Pilar Cubas
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología, CSIC-Universidad Autónoma de MadridMadrid, Spain
| | - Inés Álvarez
- Plant Evolutionary Biology Group, Real Jardín Botánico (CSIC)Madrid, Spain
| | | | - Javier Fuertes-Aguilar
- Plant Evolutionary Biology Group, Real Jardín Botánico (CSIC)Madrid, Spain
- *Correspondence: Javier Fuertes-Aguilar
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The phylogeny of Heliconia (Heliconiaceae) and the evolution of floral presentation. Mol Phylogenet Evol 2016; 117:150-167. [PMID: 27998817 DOI: 10.1016/j.ympev.2016.12.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2016] [Revised: 11/29/2016] [Accepted: 12/01/2016] [Indexed: 12/17/2022]
Abstract
Heliconia (Heliconiaceae, order Zingiberales) is among the showiest plants of the Neotropical rainforest and represent a spectacular co-evolutionary radiation with hummingbirds. Despite the attractiveness and ecological importance of many Heliconia, the genus has been the subject of limited molecular phylogenetic studies. We sample seven markers from the plastid and nuclear genomes for 202 samples of Heliconia. This represents ca. 75% of accepted species and includes coverage of all taxonomic subgenera and sections. We date this phylogeny using fossils associated with other families in the Zingiberales; in particular we review and evaluate the Eocene fossil Ensete oregonense. We use this dated phylogenetic framework to evaluate the evolution of two components of flower orientation that are hypothesized to be important for modulating pollinator discrimination and pollen placement: resupination and erect versus pendant inflorescence habit. Our phylogenetic results suggest that the monophyletic Melanesian subgenus Heliconiopsis and a small clade of Ecuadorian species are together the sister group to the rest of Heliconia. Extant diversity of Heliconia originated in the Late Eocene (39Ma) with rapid diversification through the Early Miocene, making it the oldest known clade of hummingbird-pollinated plants. Most described subgenera and sections are not monophyletic, though closely related groups of species, often defined by shared geography, mirror earlier morphological cladistic analyses. Evaluation of changes in resupination and inflorescence habit suggests that these characters are more homoplasious than expected, and this largely explains the non-monophyly of previously circumscribed subgenera, which were based on these characters. We also find strong evidence for the correlated evolution of resupination and inflorescence habit. The correlated model suggests that the most recent common ancestor of all extant Heliconia had resupinate flowers and erect inflorescences. Finally, we note our nearly complete species sampling and dated phylogeny allow for an assessment of taxonomic history in terms of phylogenetic diversity. We find approximately half of the currently recognized species, corresponding to half of the phylogenetic diversity, have been described since 1975, highlighting the continued importance of basic taxonomic research and conservation initiatives to preserve both described and undiscovered species of Heliconia.
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Liao IT, Shan H, Xu G, Zhang R. Bridging evolution and development in plants. THE NEW PHYTOLOGIST 2016; 212:827-830. [PMID: 27874986 DOI: 10.1111/nph.14294] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Affiliation(s)
- Irene T Liao
- Department of Biology, Duke University, Durham, NC, USA
| | - Hongyan Shan
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Guixia Xu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Rui Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
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Zhong J, Powell S, Preston JC. Organ boundary NAC-domain transcription factors are implicated in the evolution of petal fusion. PLANT BIOLOGY (STUTTGART, GERMANY) 2016; 18:893-902. [PMID: 27500862 DOI: 10.1111/plb.12493] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 08/05/2016] [Indexed: 05/25/2023]
Abstract
UNLABELLED Research rationale: Evolution of fused petals (sympetaly) is considered to be an important innovation that has repeatedly led to increased pollination efficiency, resulting in accelerated rates of plant diversification. Although little is known about the underlying regulation of sympetaly, genetic pathways ancestrally involved in organ boundary establishment (e.g. CUP SHAPED COTYLEDON [CUC] 1-3 genes) are strong candidates. In sympetalous petunia, mutations in the CUC1/2-like orthologue NO APICAL MERISTEM (NAM) inhibit shoot apical meristem formation. Despite this, occasional 'escape shoots' develop flowers with extra petals and fused inter-floral whorl organs. Central methods: To To determine if petunia CUC-like genes regulate additional floral patterning, we used virus-induced silencing (VIGS) following establishment of healthy shoot apices to re-examine the role of NAM in petunia petal development, and uniquely characterise the CUC3 orthologue NH16. KEY RESULTS Confirming previous results, we found that reduced floral NAM/NH16 expression caused increased petal-stamen and stamen-carpel fusion, and often produced extra petals. However, further to previous results, all VIGS plants infected with NAM or NH16 constructs exhibited reduced fusion in the petal whorl compared to control plants. MAIN CONCLUSIONS Together with previous data, our results demonstrate conservation of petunia CUC-like genes in establishing inter-floral whorl organ boundaries, as well as functional evolution to affect the fusion of petunia petals.
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Affiliation(s)
- J Zhong
- Department of Plant Biology, The University of Vermont, Burlington, VT, USA
| | - S Powell
- Department of Plant Biology, The University of Vermont, Burlington, VT, USA
| | - J C Preston
- Department of Plant Biology, The University of Vermont, Burlington, VT, USA.
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Marcellini S, González F, Sarrazin AF, Pabón-Mora N, Benítez M, Piñeyro-Nelson A, Rezende GL, Maldonado E, Schneider PN, Grizante MB, Da Fonseca RN, Vergara-Silva F, Suaza-Gaviria V, Zumajo-Cardona C, Zattara EE, Casasa S, Suárez-Baron H, Brown FD. Evolutionary Developmental Biology (Evo-Devo) Research in Latin America. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2016; 328:5-40. [PMID: 27491339 DOI: 10.1002/jez.b.22687] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Revised: 06/16/2016] [Accepted: 06/20/2016] [Indexed: 12/29/2022]
Abstract
Famous for its blind cavefish and Darwin's finches, Latin America is home to some of the richest biodiversity hotspots of our planet. The Latin American fauna and flora inspired and captivated naturalists from the nineteenth and twentieth centuries, including such notable pioneers such as Fritz Müller, Florentino Ameghino, and Léon Croizat who made a significant contribution to the study of embryology and evolutionary thinking. But, what are the historical and present contributions of the Latin American scientific community to Evo-Devo? Here, we provide the first comprehensive overview of the Evo-Devo laboratories based in Latin America and describe current lines of research based on endemic species, focusing on body plans and patterning, systematics, physiology, computational modeling approaches, ecology, and domestication. Literature searches reveal that Evo-Devo in Latin America is still in its early days; while showing encouraging indicators of productivity, it has not stabilized yet, because it relies on few and sparsely distributed laboratories. Coping with the rapid changes in national scientific policies and contributing to solve social and health issues specific to each region are among the main challenges faced by Latin American researchers. The 2015 inaugural meeting of the Pan-American Society for Evolutionary Developmental Biology played a pivotal role in bringing together Latin American researchers eager to initiate and consolidate regional and worldwide collaborative networks. Such networks will undoubtedly advance research on the extremely high genetic and phenotypic biodiversity of Latin America, bound to be an almost infinite source of amazement and fascinating findings for the Evo-Devo community.
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Affiliation(s)
- Sylvain Marcellini
- Laboratorio de Desarrollo y Evolución, Departamento de Biología Celular, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | - Favio González
- Facultad de Ciencias, Instituto de Ciencias Naturales, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Andres F Sarrazin
- Instituto de Química, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | | | - Mariana Benítez
- Laboratorio Nacional de Ciencias de la Sostenibilidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Alma Piñeyro-Nelson
- Departamento de Producción Agrícola y Animal, Universidad Autónoma Metropolitana, Xochimilco, Ciudad de México, México
| | - Gustavo L Rezende
- Universidade Estadual do Norte Fluminense, CBB, LQFPP, Campos dos Goytacazes, RJ, Brazil
| | - Ernesto Maldonado
- EvoDevo Lab, Unidad de Sistemas Arrecifales, Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Puerto Morelos, Quintana Roo, México
| | | | | | - Rodrigo Nunes Da Fonseca
- Núcleo em Ecologia e Desenvolvimento SócioAmbiental de Macaé (NUPEM), Campus Macaé, Universidade Federal do Rio de Janeiro, Macae, RJ, Brazil
| | | | | | | | | | - Sofia Casasa
- Department of Biology, Indiana University, Bloomington, IN, USA
| | | | - Federico D Brown
- Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil
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Arango-Ocampo C, González F, Alzate JF, Pabón-Mora N. The developmental and genetic bases of apetaly in Bocconia frutescens (Chelidonieae: Papaveraceae). EvoDevo 2016; 7:16. [PMID: 27489612 DOI: 10.1186/s1322701600546] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2016] [Accepted: 07/19/2016] [Indexed: 05/28/2023] Open
Abstract
BACKGROUND Bocconia and Macleaya are the only genera of the poppy family (Papaveraceae) lacking petals; however, the developmental and genetic processes underlying such evolutionary shift have not yet been studied. RESULTS We studied floral development in two species of petal-less poppies Bocconia frutescens and Macleaya cordata as well as in the closely related petal-bearing Stylophorum diphyllum. We generated a floral transcriptome of B. frutescens to identify MADS-box ABCE floral organ identity genes expressed during early floral development. We performed phylogenetic analyses of these genes across Ranunculales as well as RT-PCR and qRT-PCR to assess loci-specific expression patterns. We found that petal-to-stamen homeosis in petal-less poppies occurs through distinct developmental pathways. Transcriptomic analyses of B. frutescens floral buds showed that homologs of all MADS-box genes are expressed except for the APETALA3-3 ortholog. Species-specific duplications of other ABCE genes in B. frutescens have resulted in functional copies with expanded expression patterns than those predicted by the model. CONCLUSIONS Petal loss in B. frutescens is likely associated with the lack of expression of AP3-3 and an expanded expression of AGAMOUS. The genetic basis of petal identity is conserved in Ranunculaceae and Papaveraceae although they have different number of AP3 paralogs and exhibit dissimilar floral groundplans.
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Affiliation(s)
| | - Favio González
- Instituto de Ciencias Naturales, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Juan Fernando Alzate
- Centro de Secuenciación Genómica Nacional (CSGN), Sede de Investigación Universitaria, Universidad de Antioquia, Medellín, Colombia
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Arango-Ocampo C, González F, Alzate JF, Pabón-Mora N. The developmental and genetic bases of apetaly in Bocconia frutescens (Chelidonieae: Papaveraceae). EvoDevo 2016; 7:16. [PMID: 27489612 PMCID: PMC4971710 DOI: 10.1186/s13227-016-0054-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2016] [Accepted: 07/19/2016] [Indexed: 01/01/2023] Open
Abstract
Background Bocconia and Macleaya are the only genera of the poppy family (Papaveraceae) lacking petals; however, the developmental and genetic processes underlying such evolutionary shift have not yet been studied. Results We studied floral development in two species of petal-less poppies Bocconiafrutescens and Macleayacordata as well as in the closely related petal-bearing Stylophorum diphyllum. We generated a floral transcriptome of B. frutescens to identify MADS-box ABCE floral organ identity genes expressed during early floral development. We performed phylogenetic analyses of these genes across Ranunculales as well as RT-PCR and qRT-PCR to assess loci-specific expression patterns. We found that petal-to-stamen homeosis in petal-less poppies occurs through distinct developmental pathways. Transcriptomic analyses of B. frutescens floral buds showed that homologs of all MADS-box genes are expressed except for the APETALA3-3 ortholog. Species-specific duplications of other ABCE genes in B. frutescens have resulted in functional copies with expanded expression patterns than those predicted by the model. Conclusions Petal loss in B. frutescens is likely associated with the lack of expression of AP3-3 and an expanded expression of AGAMOUS. The genetic basis of petal identity is conserved in Ranunculaceae and Papaveraceae although they have different number of AP3 paralogs and exhibit dissimilar floral groundplans. Electronic supplementary material The online version of this article (doi:10.1186/s13227-016-0054-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Favio González
- Instituto de Ciencias Naturales, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Juan Fernando Alzate
- Centro de Secuenciación Genómica Nacional (CSGN), Sede de Investigación Universitaria, Universidad de Antioquia, Medellín, Colombia
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Sasaki K, Yamaguchi H, Kasajima I, Narumi T, Ohtsubo N. Generation of Novel Floral Traits Using a Combination of Floral Organ-Specific Promoters and a Chimeric Repressor in Torenia fournieri Lind. PLANT & CELL PHYSIOLOGY 2016; 57:1319-31. [PMID: 27107289 DOI: 10.1093/pcp/pcw081] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 04/12/2016] [Indexed: 05/02/2023]
Abstract
In this study, we attempted to develop a new biotechnological method for the efficient modification of floral traits. Because transcription factors play an important role in determining floral traits, chimeric repressors, which are generated by attaching a short transcriptional repressor domain to transcription factors, have been widely used as effective tools for modifying floral traits in many plant species. However, the overexpression of these chimeric repressors by the Cauliflower mosaic virus 35S promoter sometimes causes undesirable morphological alterations to other organs. We attempted simultaneously to generate new floral traits and avoid such quality loss by examining five additional floral organ-specific promoters, one Arabidopsis thaliana promoter and four Torenia fournieri promoters, for the expression of the chimeric repressor of Arabidopsis TCP3 (AtTCP3), whose overexpression drastically alters floral traits but also generates dwarf phenotypes and deformed leaves. We found that the four torenia promoters exhibited particularly strong activity in the petals but not in the leaves, and that the combination of these floral organ-specific promoters with the chimeric repressor of AtTCP3 caused changes in the color, color patterns and cell shapes of petals, whilst avoiding other unfavorable phenotypes. Interestingly, each promoter that we used in this study generated characteristic and distinguishable floral traits. Thus, the use of different floral organ-specific promoters with different properties enables us to generate diverse floral traits using a single chimeric repressor without changing the phenotypes of other organs.
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Affiliation(s)
- Katsutomo Sasaki
- Institute of Vegetable and Floriculture Science, National Agriculture and Food Research Organization (NARO), Fujimoto 2-1, Tsukuba, Ibaraki, 305-8519 Japan
| | - Hiroyasu Yamaguchi
- Institute of Vegetable and Floriculture Science, National Agriculture and Food Research Organization (NARO), Fujimoto 2-1, Tsukuba, Ibaraki, 305-8519 Japan
| | - Ichiro Kasajima
- Institute of Vegetable and Floriculture Science, National Agriculture and Food Research Organization (NARO), Fujimoto 2-1, Tsukuba, Ibaraki, 305-8519 Japan
| | - Takako Narumi
- Institute of Vegetable and Floriculture Science, National Agriculture and Food Research Organization (NARO), Fujimoto 2-1, Tsukuba, Ibaraki, 305-8519 Japan Graduate School of Agriculture, Kagawa University, 2393 Ikenobe, Miki-cho, Kita-gun, Kagawa, 761-0795 Japan
| | - Norihiro Ohtsubo
- Institute of Vegetable and Floriculture Science, National Agriculture and Food Research Organization (NARO), Fujimoto 2-1, Tsukuba, Ibaraki, 305-8519 Japan Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Shimogamohangi-cho, Sakyo-ku, Kyoto, 606-8522 Japan
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Gardner AG, Fitz Gerald JN, Menz J, Shepherd KA, Howarth DG, Jabaily RS. Characterizing Floral Symmetry in the Core Goodeniaceae with Geometric Morphometrics. PLoS One 2016; 11:e0154736. [PMID: 27148960 PMCID: PMC4858217 DOI: 10.1371/journal.pone.0154736] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 04/18/2016] [Indexed: 11/19/2022] Open
Abstract
Core Goodeniaceae is a clade of ~330 species primarily distributed in Australia. Considerable variation in flower morphology exists within this group and we aim to use geometric morphometrics to characterize this variation across the two major subclades: Scaevola sensu lato (s.l.) and Goodenia s.l., the latter of which was hypothesized to exhibit greater variability in floral symmetry form. We test the hypothesis that floral morphological variation can be adequately characterized by our morphometric approach, and that discrete groups of floral symmetry morphologies exist, which broadly correlate with subjectively determined groups. From 335 images of 44 species in the Core Goodeniaceae, two principal components were computed that describe >98% of variation in all datasets. Increasing values of PC1 ventralize the dorsal petals (increasing the angle between them), whereas increasing values of PC2 primarily ventralize the lateral petals (decreasing the angle between them). Manipulation of these two morphological “axes” alone was sufficient to recreate any of the general floral symmetry patterns in the Core Goodeniaceae. Goodenia s.l. exhibits greater variance than Scaevola s.l. in PC1 and PC2, and has a significantly lower mean value for PC1. Clustering clearly separates fan-flowers (with dorsal petals at least 120° separated) from the others, whereas the distinction between pseudo-radial and bilabiate clusters is less clear and may form a continuum rather than two distinct groups. Transitioning from the average fan-flower to the average non-fan-flower is described almost exclusively by PC1, whereas PC2 partially describes the transition between bilabiate and pseudo-radial morphologies. Our geometric morphometric method accurately models Core Goodeniaceae floral symmetry diversity.
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Affiliation(s)
- Andrew G. Gardner
- Department of Biology, Rhodes College, 2000 N. Parkway, Memphis, Tennessee, United States of America
- * E-mail:
| | - Jonathan N. Fitz Gerald
- Department of Biology, Rhodes College, 2000 N. Parkway, Memphis, Tennessee, United States of America
| | - John Menz
- Department of Biology, Rhodes College, 2000 N. Parkway, Memphis, Tennessee, United States of America
| | - Kelly A. Shepherd
- Science and Conservation Division, Department of Parks and Wildlife, Kensington, Western Australia, Australia
| | - Dianella G. Howarth
- Department of Biological Sciences, St. John’s University, Queens, New York, United States of America
| | - Rachel S. Jabaily
- Department of Biology, Rhodes College, 2000 N. Parkway, Memphis, Tennessee, United States of America
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Zhang H, Liu F, Wang R, Liu J. Roles of Clonal Integration in both Heterogeneous and Homogeneous Habitats. FRONTIERS IN PLANT SCIENCE 2016; 7:551. [PMID: 27200026 DOI: 10.1086/687225] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Accepted: 04/11/2016] [Indexed: 05/27/2023]
Abstract
Many studies have shown that clonal integration can promote the performance of clonal plants in heterogeneous habitats, but the roles of clonal integration in both heterogeneous and homogeneous habitats were rarely studied simultaneously. Ramet pairs of Alternanthera philoxeroides (Mart.) Griseb were placed in two habitats either heterogeneous or homogeneous in soil nutrient availability, with stolon connections left intact or severed. Total biomass, total length of stolons, and number of new ramets of distal (relatively young) ramets located in low-nutrient environments were significantly greater when the distal ramets were connected to than when they were disconnected from proximal (relatively old) ramets located in high-nutrient environments. Total length of stolons of proximal ramets growing in low-nutrient environments was significantly higher when the proximal ramets were connected to than when they were disconnected from the distal ramets growing in high-nutrient environments, but stolon connection did not affect total biomass or number of new ramets of the proximal ramets. Stolon severing also did not affect the growth of the whole ramet pairs in heterogeneous environments. In homogeneous high-nutrient environments stolon severing promoted the growth of the proximal ramets and the ramet pairs, but in homogeneous low-nutrient environments it did not affect the growth of the proximal or distal ramets. Hence, for A. philoxeroides, clonal fragmentation appears to be more advantageous than clonal integration in resource-rich homogeneous habitats, and clonal integration becomes beneficial in heterogeneous habitats. Our study contributes to revealing roles of clonal integration in both heterogeneous and homogeneous habitats and expansion patterns of invasive clonal plants such as A. philoxeroides in multifarious habitats.
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Affiliation(s)
- Haijie Zhang
- Institute of Environmental Research, Shandong University Jinan, China
| | - Fenghong Liu
- National Science Library, Chinese Academy of Sciences Beijing, China
| | - Renqing Wang
- Institute of Environmental Research, Shandong UniversityJinan, China; School of Life Sciences, Shandong UniversityJinan, China
| | - Jian Liu
- Institute of Environmental Research, Shandong University Jinan, China
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Endress PK. Development and evolution of extreme synorganization in angiosperm flowers and diversity: a comparison of Apocynaceae and Orchidaceae. ANNALS OF BOTANY 2016; 117:749-67. [PMID: 26292994 PMCID: PMC4845794 DOI: 10.1093/aob/mcv119] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Accepted: 06/22/2015] [Indexed: 05/04/2023]
Abstract
BACKGROUND AND AIMS Apocynaceae and Orchidaceae are two angiosperm families with extreme flower synorganization. They are unrelated, the former in eudicots, the latter in monocots, but they converge in the formation of pollinia and pollinaria, which do not occur in any other angiosperm family, and for which extreme synorganization of floral organs is a precondition. In each family extensive studies on flower development and evolution have been performed; however, newer comparative studies focusing on flower synorganization and involving both families together are lacking. SCOPE For this study an extensive search through the morphological literature has been conducted. Based on this and my own studies on flowers in various Apocynaceae and Orchidaceae and complex flowers in other angiosperms with scanning electron microscopy and with microtome section series, a review on convergent floral traits in flower development and architecture in the two families is presented. KEY FINDINGS There is a tendency of protracted development of synorganized parts in Apocynaceae and Orchidaceae (development of synorganization of two or more organs begins earlier the more accentuated it is at anthesis). Synorganization (or complexity) also paves the way for novel structures. One of the most conspicuous such novel structures in Apocynaceae is the corona, which is not the product of synorganization of existing organs; however, it is probably enhanced by synorganization of other, existing, floral parts. In contrast to synorganized parts, the corona appears developmentally late. CONCLUSIONS Synorganization of floral organs may lead to a large number of convergences in clades that are only very distantly related. The convergences that have been highlighted in this comparative study should be developmentally investigated directly in parallel in future studies.
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Affiliation(s)
- Peter K Endress
- Institute of Systematic Botany, University of Zurich, Zollikerstrasse 107, 8008 Zurich, Switzerland
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Berger BA, Thompson V, Lim A, Ricigliano V, Howarth DG. Elaboration of bilateral symmetry across Knautia macedonica capitula related to changes in ventral petal expression of CYCLOIDEA-like genes. EvoDevo 2016; 7:8. [PMID: 27042288 PMCID: PMC4818532 DOI: 10.1186/s13227-016-0045-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Accepted: 02/10/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Shifts in floral form across angiosperms, particularly from radially symmetrical to bilaterally symmetrical flowers, are often associated with shifts in speciation rates and changes in pollination syndrome. Growing evidence across both rosids and asterids indicates that CYCLOIDEA (CYC)-like transcription factors from the TCP gene family play a role in establishing the dorsoventral pattern of flower symmetry, which affects the development of both the corolla and androecium. Previous studies of CYC-like genes, especially of the CYC2 clade, indicate that these genes are dorsally restricted in bilaterally symmetrical flowers. Also, gene duplication of CYC-like genes often correlates with shifts in floral form in both individual flowers and head-like inflorescences (capitula). RESULTS Here, we compared the expression patterns of six CYC-like genes from dorsal, lateral, and ventral petals of internal and external florets across capitula of Knautia macedonica (Dipsacaceae). We demonstrate that multiple copies of CYC-like genes are differentially expressed among petal types and between internal and external florets. Across paralogs, there was a general trend toward a reduction in dorsal expression and an increase in ventral expression in internal florets compared to external florets. However, it was in the ventral petals where a statistically significant increase in expression correlates with a less zygomorphic flower. We also show for the first time lateral-specific expression of a CYC-like gene. Additionally, dorsoventral asymmetric expression of a CYC3 paralog indicates that this understudied gene clade is likely also involved in floral symmetry. CONCLUSIONS These data indicate that the elaboration of bilateral symmetry may be regulated by the dorsoventral gradient of expression, with statistically significant changes in ventral expression correlating with changes in dorsoventral morphological specialization.
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Affiliation(s)
- Brent A Berger
- Department of Botany, University of Wisconsin-Madison, 430 Lincoln Dr., Madison, WI 53706 USA ; Department of Biological Sciences, St. John's University, 8000 Utopia Parkway, Queens, NY 11439 USA
| | - Veronica Thompson
- Department of Biological Sciences, St. John's University, 8000 Utopia Parkway, Queens, NY 11439 USA
| | - Aedric Lim
- Department of Biological Sciences, St. John's University, 8000 Utopia Parkway, Queens, NY 11439 USA
| | - Vincent Ricigliano
- Department of Biological Sciences, St. John's University, 8000 Utopia Parkway, Queens, NY 11439 USA
| | - Dianella G Howarth
- Department of Biological Sciences, St. John's University, 8000 Utopia Parkway, Queens, NY 11439 USA
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Zhong J, Preston JC. Bridging the gaps: evolution and development of perianth fusion. THE NEW PHYTOLOGIST 2015; 208:330-335. [PMID: 26094556 DOI: 10.1111/nph.13517] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Accepted: 04/17/2015] [Indexed: 06/04/2023]
Abstract
One of the most striking innovations in flower development is the congenital or postgenital union of petals (sympetaly) which has enabled dramatic specialization in flower structure and possibly accelerated speciation rates. Sympetalous flowers exhibit extraordinary variation in development, including the degree and timing of fusion, and fusion with other floral organs. Different axes of corolla tube complexity can be disentangled at the developmental level, with most variation being explained by differences in coordinated growth between interconnected and lobed regions of neighboring petal primordia, and between lower and upper portions of the corolla tube, defined by the stamen insertion boundary. Genetically, inter- and intra-specific variation in the degree of petal fusion is controlled by various inputs from genes that affect organ boundary and lateral growth, signaling between different cell types, and production of the cuticle. It is thus hypothesized that the evolution and diversification of fused petals, at least within the megadiverse Asteridae clade of core eudicots, have occurred through the modification of a conserved genetic pathway previously involved in free petal development.
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Affiliation(s)
- Jinshun Zhong
- Department of Plant Biology, University of Vermont, Burlington, VT, 05405, USA
| | - Jill C Preston
- Department of Plant Biology, University of Vermont, Burlington, VT, 05405, USA
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Mason PH, Domínguez D JF, Winter B, Grignolio A. Hidden in plain view: degeneracy in complex systems. Biosystems 2014; 128:1-8. [PMID: 25543071 DOI: 10.1016/j.biosystems.2014.12.003] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Revised: 12/20/2014] [Accepted: 12/23/2014] [Indexed: 12/27/2022]
Abstract
Degeneracy is a word with two meanings. The popular usage of the word denotes deviance and decay. In scientific discourse, degeneracy refers to the idea that different pathways can lead to the same output. In the biological sciences, the concept of degeneracy has been ignored for a few key reasons. Firstly, the word "degenerate" in popular culture has negative, emotionally powerful associations that do not inspire scientists to consider its technical meaning. Secondly, the tendency of searching for single causes of natural and social phenomena means that scientists can overlook the multi-stranded relationships between cause and effect. Thirdly, degeneracy and redundancy are often confused with each other. Degeneracy refers to dissimilar structures that are functionally similar while redundancy refers to identical structures. Degeneracy can give rise to novelty in ways that redundancy cannot. From genetic codes to immunology, vaccinology and brain development, degeneracy is a crucial part of how complex systems maintain their functional integrity. This review article discusses how the scientific concept of degeneracy was imported into genetics from physics and was later introduced to immunology and neuroscience. Using examples of degeneracy in immunology, neuroscience and linguistics, we demonstrate that degeneracy is a useful way of understanding how complex systems function. Reviewing the history and theoretical scope of degeneracy allows its usefulness to be better appreciated, its coherency to be further developed, and its application to be more quickly realized.
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Affiliation(s)
- P H Mason
- Woolcock Institute of Medical Research, University of Sydney, 431 Glebe Point Road, Glebe, 2037 NSW, Australia.
| | - J F Domínguez D
- Experimental Neuropsychology Research Unit, School of Psychological Sciences, Monash University, Australia
| | - B Winter
- Cognitive and Information Sciences, University of California, Merced 5200 North Lake Rd., Merced, CA 95343, USA
| | - A Grignolio
- Section and Museum of History of Medicine, University of Rome "La Sapienza", viale dell'Università, 34a 00185 Rome, Italy
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